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Long non-coding mRNA

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https://www.readbyqxmd.com/read/28442363/the-global-expression-profiling-in-esophageal-squamous-cell-carcinoma
#1
Fuqiang Dai, Longyong Mei, Shenglan Meng, Zheng Ma, Wei Guo, Jinghai Zhou, Jingge Zhang
Esophageal squamous cell carcinoma (ESCC) is the dominant subtype of esophageal cancer worldwide. This study aimed to explore the aberrant global expression profiling and construct regulatory network in ESCC for understanding tumorigenesis of ESCC. The expression pattern of long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA was measured by RNA-sequencing in ESCC. Differentially expressed lncRNAs/miRNAs/mRNAs (DELs/DEMs/DEMIs) were identified in ESCC. DEMIs-DEMs network was constructed; hsa-miR-424-5p and hsa-miR-450b-5p were the hub miRNAs in the network, which negatively regulated 19 and 17 DEMs...
April 22, 2017: Genomics
https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#2
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28440471/time-dependent-differential-expression-of-long-non-coding-rnas-following-peripheral-nerve-injury
#3
Bin Pan, Heng-Xing Zhou, Yi Liu, Jia-Yin Yan, Yao Wang, Xue Yao, Yan-Qiu Deng, Shu-Yi Chen, Lu Lu, Zhi-Jian Wei, Xiao-Hong Kong, Shi-Qing Feng
Long non-coding RNAs (lncRNAs) are widely accepted as key players in various biological processes. However, the roles of lncRNA in peripheral nerve regeneration remain completely unknown. Thus, in this study, we performed microarray analysis to measure lncRNA expression in the distal segment of the sciatic nerve at 0, 3, 7 and 14 days following injury. We identified 5,354 lncRNAs that were differentially expressed: 3,788 lncRNAs were differentially expressed between days 0 and 3; 3,314 lncRNAs were differentially expressed between days 0 and 7; and 2,400 lncRNAs were differentially expressed between days 0 and 14...
April 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28428329/visualization-of-rna-structure-models-within-the-integrative-genomics-viewer
#4
Steven Busan, Kevin M Weeks
Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist...
April 20, 2017: RNA
https://www.readbyqxmd.com/read/28423647/upregulation-of-the-lncrna-meg3-induces-autophagy-to-inhibit-tumorigenesis-and-progression-of-epithelial-ovarian-carcinoma-by-regulating-activity-of-atg3
#5
Yin-Ling Xiu, Kai-Xuan Sun, Xi Chen, Shuo Chen, Yang Zhao, Qing-Guo Guo, Zhi-Hong Zong
Maternally expressed gene 3 (Meg3), a long non-coding RNA, has been reported to be associated with the pathogenesis of multiple malignancies. However, little is known regarding the role of Meg3 in epithelial ovarian cancer (EOC). In this study, we found that the expression of Meg3 was lower in epithelial ovarian carcinoma, and has potential to be considered as a biomarker for ovarian cancer. After transfecting the ovarian cancer cell lines OVCAR3 and A2780 with Meg3, phenotypic changes and autophagy-related molecules were examined...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#6
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28420760/novel-lnc-rna-regulated-by-hif-1-inhibits-apoptotic-cell-death-in-the-renal-tubular-epithelial-cells-under-hypoxia
#7
Imari Mimura, Yosuke Hirakawa, Yasuharu Kanki, Natsuki Kushida, Ryo Nakaki, Yutaka Suzuki, Tetsuhiro Tanaka, Hiroyuki Aburatani, Masaomi Nangaku
Chronic tubulointerstitial hypoxia plays an important role as the final common pathway to end-stage renal disease. HIF-1 (hypoxia-inducible factor-1) is a master transcriptional factor under hypoxia, regulating downstream target genes. Genome-wide analysis of HIF-1 binding sites using high-throughput sequencers has clarified various kinds of downstream targets and made it possible to demonstrate the novel roles of HIF-1. Our aim of this study is to identify novel HIF-1 downstream epigenetic targets which may play important roles in the kidney...
April 2017: Physiological Reports
https://www.readbyqxmd.com/read/28417961/high-throughput-sequencing-and-co-expression-network-analysis-of-lncrnas-and-mrnas-in-early-brain-injury-following-experimental-subarachnoid-haemorrhage
#8
Jianhua Peng, Yue Wu, Xiaocui Tian, Jinwei Pang, Li Kuai, Fang Cao, Xinghu Qin, Jianjun Zhong, Xinshen Li, Yong Li, Xiaochuan Sun, Ligang Chen, Yong Jiang
Subarachnoid haemorrhage (SAH) is a fatal neurovascular disease following cerebral aneurysm rupture with high morbidity and mortality rates. Long non-coding RNAs (lncRNAs) are a type of mammalian genome transcript, are abundantly expressed in the brain and are involved in many nervous system diseases. However, little is currently known regarding the influence of lncRNAs in early brain injury (EBI) after SAH. This study analysed the expression profiles of lncRNAs and mRNAs in SAH brain tissues of mice using high-throughput sequencing...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415801/identification-of-long-non-coding-rnas-that-stimulate-cell-survival-in-bladder-cancer
#9
Aleksandra M Dudek, Sabrina J Boer, Nanda Boon, J Alfred Witjes, Lambertus A L M Kiemeney, Gerald W Verhaegh
For many years, research on the biology underlying bladder cancer focused on protein-coding genes which cover only about 3% of the human genome. Recently, it was discovered that a large part of the human genome is actively transcribed as long non-coding RNAs (lncRNAs). LncRNAs are master regulators of gene expression and several lncRNAs were shown to play a role in bladder cancer development and progression. Here, we analyzed lncRNA expression in muscle-invasive bladder cancer (MIBC) using the MiTranscriptome database of cancer lncRNA expression profiles, and we studied their function in bladder cancer-derived tumor cells...
March 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28415620/integrated-analysis-profiles-of-long-non-coding-rnas-reveal-potential-biomarkers-of-drug-resistance-in-lung-cancer
#10
Wenhua Xue, Lifeng Li, Xin Tian, Zhirui Fan, Ying Yue, Chaoqi Zhang, Xianfei Ding, Xiaoqin Song, Bingjun Ma, Yunkai Zhai, Jingli Lu, Quancheng Kan, Jie Zhao
Lung cancer is one of the leading causes of cancer-related death. Resistance to chemotherapy and molecularly targeted therapies is a major problem that can contribute substantially to high mortality. The roles of long non-coding RNAs (lncRNAs) in drug resistance of lung cancer are insufficiently understood. Here, we identified a distinct drug resistance-related transcriptional signature and constructed a functional lncRNA-mRNA co-expression network. We found that 34 lncRNAs and 103 mRNAs have differential expression in drug resistance of lung cancer, in which 10 lncRNAs were down regulated and 24 up regulated; 49 mRNAs were down regulated and 54 up regulated...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28403886/the-long-non-coding-rna-tp73-as1-modulates-hcc-cell-proliferation-through-mir-200a-dependent-hmgb1-rage-regulation
#11
Shaling Li, Yan Huang, Yun Huang, Yongming Fu, Daolin Tang, Rui Kang, Rongrong Zhou, Xue-Gong Fan
BACKGROUND: P73 antisense RNA 1 T (non-protein coding), also known as TP73-AS1, is a long non-coding RNA (lncRNA) which is involved in cell proliferation and the development of tumors. However, the exact effects and molecular mechanisms of TP73-AS1 in hepatocellular carcinoma (HCC) progression are still unknown. The present study is aimed to investigate the detailed functions and the mechanism of TP73-AS1 in regulation of HCC cell proliferation. METHODS: TP73-AS1 expression in HCC tissues and cell lines was determined using real-time PCR assays; the correlation of TP73-AS1 expression with clinicopathological features of HCC was analyzed...
April 12, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28400335/review-regulation-of-the-cancer-epigenome-by-long-non-coding-rnas
#12
Megan E Forrest, Ahmad M Khalil
Long non-coding RNAs have emerged as highly versatile players in the regulation of gene expression in development and human disease, particularly cancer. Hundreds of lncRNAs become dysregulated across tumor types, and multiple lncRNAs have demonstrated functions as tumor-suppressors or oncogenes. Furthermore, studies have demonstrated that dysregulation of lncRNAs results in alterations of the epigenome in cancer cells, potentially providing a novel mechanism for the massive epigenomic alterations observed in many tumors...
April 9, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28396617/long-non-coding-rna-malat1-drives-gastric-cancer-progression-by-regulating-hmgb2-modulating-the-mir-1297
#13
Jijun Li, Jinghua Gao, Wen Tian, Yongsheng Li, Jinghua Zhang
BACKGROUND: Emerging evidences have verified that long non-coding RNAs (lncRNAs) play important regulatory roles in the pathogenesis and progression of cancers. lncRNAs metastasis associated lung adenocarcinoma transcript 1 (MALAT1) have been found to be up-regulated in some human cancers. The main objective of this study was to investigate the expression level and biological function of MALAT1 in gastric cancer (GC). METHODS: Quantificational real-time polymerase chain reaction (qRT-PCR) was performed to detect the mRNA levels of MALAT1 in 78 paired gastric carcinoma tissues and adjacent normal tissues, and the associations of MALAT1 expression with the clinicopathological features were analyzed, and the prognosis of gastric carcinoma patients was evaluated...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28388877/evolutionary-acquisition-of-promoter-associated-non-coding-rna-pancrna-repertoires-diversifies-species-dependent-gene-activation-mechanisms-in-mammals
#14
Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura
BACKGROUND: Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activate the partner gene expression via local epigenetic changes. RESULTS: Here, we identify thousands of genes under pancRNA-mediated transcriptional activation in five mammalian species in common. In the mouse, 1) pancRNA-partnered genes confined their expression pattern to certain tissues compared to pancRNA-lacking genes, 2) expression of pancRNAs was significantly correlated with the enrichment of active chromatin marks, H3K4 trimethylation and H3K27 acetylation, at the promoter regions of the partner genes, 3) H3K4me1 marked the pancRNA-partnered genes regardless of their expression level, and 4) C- or G-skewed motifs were exclusively overrepresented between-200 and-1 bp relative to the transcription start sites of the pancRNA-partnered genes...
April 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28385905/in-vivo-characterization-of-an-ahr-dependent-long-non-coding-rna-required-for-proper-sox9b-expression
#15
Gloria R Garcia, Britton C Goodale, Michelle W Wiley, Jane K La Du, David A Hendrix, Robert L Tanguay
Xenobiotic activation of the aryl hydrocarbon receptor (AHR) by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) prevents the proper formation of craniofacial cartilage and the heart in developing zebrafish. Downstream molecular targets responsible for AHR-dependent adverse effects remain largely unknown; however, in zebrafish sox9b has been identified as one of the most reduced transcripts in several target organs and is hypothesized to have a causal role in TCDD-induced toxicity. The reduction of sox9b expression in TCDD-exposed zebrafish embryos has been shown to contribute to heart and jaw malformation phenotypes...
April 6, 2017: Molecular Pharmacology
https://www.readbyqxmd.com/read/28377111/genome-wide-identification-of-micrornas-involved-in-fatty-acid-and-lipid-metabolism-of-brassica-napus-by-small-rna-and-degradome-sequencing
#16
Zhiwei Wang, Yan Qiao, Jingjing Zhang, Wenhui Shi, Jinwen Zhang
Rapeseed (Brassica napus) is an important cash crop considered as the third largest oil crop worldwide. Rapeseed oil contains various saturation or unsaturation fatty acids, these fatty acids, whose could incorporation with TAG form into lipids stored in seeds play various roles in the metabolic activity. The different fatty acids in B. napus seeds determine oil quality, define if the oil is edible or must be used as industrial material. miRNAs are kind of non-coding sRNAs that could regulate gene expressions through post-transcriptional modification to their target transcripts playing important roles in plant metabolic activities...
April 1, 2017: Gene
https://www.readbyqxmd.com/read/28376901/down-regulation-of-lncrna-tug1-enhances-radiosensitivity-in-bladder-cancer-via-suppressing-hmgb1-expression
#17
Huijuan Jiang, Xigang Hu, Hongzhi Zhang, Wenbo Li
BACKGROUND: Long non-coding RNAs (lncRNAs) have been reported to regulate the sensitivity of different cancer cells to chemoradiotherapy. Aberrant expression of lncRNA Taurine-upregulated gene 1 (TUG1) has been found to be involved in the development of bladder cancer, however, its function and underlying mechanism in the radioresistance of bladder cancer remains unclear. METHODS: Quantitative real-time PCR (qRT-PCR) was conducted to measure the expression of TUG1 and HMGB1 mRNA in bladder cancer tissues and cell lines...
April 4, 2017: Radiation Oncology
https://www.readbyqxmd.com/read/28364379/micror-545-mediates-colorectal-cancer-cells-proliferation-through-up-regulating-epidermal-growth-factor-receptor-expression-in-hotair-long-non-coding-rna-dependent
#18
Xinli Huang, Sen Lu
The functional impact of recently discovered miRNAs in human cancer remains to be clarified. One miRNA in colorectal cancer which has attracted attention is miR-545. In this study, we examined the function of miR-545 in proliferation of colorectal cancer cells. Expressions of HOTAIR, miRNA-545, and epidermal growth factor receptor (EGFR) mRNA were measured in 100 paired cancerous and non-cancerous tissues as well as in SW480 and LOVO colorectal cancer cell (CRC) lines by quantitative RT-PCR. The relative protein level of EGFR was measured using western blotting...
March 31, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28358263/lncrna-ccat1-modulates-the-sensitivity-of-paclitaxel-in-nasopharynx-cancers-cells-via-mir-181a-cpeb2-axis
#19
Qiaosu Wang, Wenjing Zhang, Shaojuan Hao
Recent studies reported that long non-coding RNA (lncRNA) might play critical roles in regulating chemo-resistant of multiple types of cancer. This study aimed to investigate whether long non-coding RNA CCAT1 was involved in Paclitaxel resistance in nasopharyngeal carcinoma (NPC). qRT-PCR was used for testing the expression of CCAT1, miR-181a and CPEB2 in tumor tissues and NPC cancers. NPC cells were transfected with siRNAs to suppress the mRNA level of CCAT1 in NPC cells. MTT assays and flow cytometry analysis were used to assess the sensitivity of paclitaxel in NPC cells...
April 18, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28350082/hotair-upregulates-an-18-gene-cell-cycle-related-mrna-network-in-glioma
#20
Kai Huang, Jia Sun, Chao Yang, Yunfei Wang, Bingcong Zhou, Chunsheng Kang, Lei Han, Qixue Wang
HOTAIR is a tumor promoting long non-coding RNA (lncRNA) with roles in multiple cancers. However, the role of HOTAIR in glioma has not been well charaterized. Genes that positively correlated with HOTAIR were identified from the Chinese Glioma Genome Atlas and constructed into an interacting network. In total, 18 genes with P-values <0.01 were further extracted and constructed into a subnetwork. Real-time PCR, western blot and immunofluorescence analyses were employed to examine the expression of the genes after HOTAIR overexpression or knockdown...
March 7, 2017: International Journal of Oncology
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